Artie Vs The Intersect v2
by Artana Stole My Heart
Summary: AU Artana story based after S2 of Chuck. Basically it is Chuck with Glee characters. ABANDONED
1. Disclaimer

**DISCLAIMER!**

**Basically this is an AU Artana story based in the Chuck Universe.**

**Knowledge of season 1 & 2 of Chuck is needed.**

**This is also a refurbished version of the first story I ever wrote so the quality of writing and style are very different from what I do now.**

**It is in script format.**

**This is an experimental story I will post the first 3 chapters over the next 3 days and depending on how well they are received I will continue to post.**


	2. The Aftermath

_Three weeks after the Hudson's wedding 3 shadowy character are in undisclosed location debriefing with General Sylvester._

**Sue**

"Santana, my deepest sympathies for your lost. He was an asset to his country and will be missed."

**Santana**

"Yes he was. So what is our next mission General?"

**Sue**

"Well Agent Lopez, you will be boarding a plane to Morocco at twenty-two hundred hours. Colonel Puckerman you will be returning to your unit in…"

**Artie**

"No they won't."

**Sue**

"Excuse me Mister Abrams."

**Artie**

"You see General I need them here because I can't live without them."

**Santana**

"We have our orders Artie and you cannot stop that."

**Artie**

"Actually I can, General I wonder how the president would feel about what happened in Tanzania seven years ago.

**Sue**

"How do you…"

**Artie**

"Over the past couple of years I learned how to access the intel in the Intersect and wouldn't you know it there was some pretty interesting stuff in your files General."

_Just then Artie's iphone rings, it was his father._

**Artie**

"Hey dad what's up?"

**Will**

"Artie I have great news." _(many weird sounds pass over the phone, Artie collapses)_ "I made an auditory Intersect."

**Santana**

"Oh my god, Artie are you alright?"

_Artie comes to._

**Artie**

"I think so, dad what just happened?"

**Will**

"I just gave you the greatest gift a father can give. The ability to be with the one you love."

_Then the General's cell ring to the tone of "Sweet Caroline" by Neil Diamond. Artie feels a very familiar feeling._

**Artie**

"Neil Diamond was an undercover agent for the Russian Government"

**Puck**

"What?"

**Sue**

"Before you even ask Agent Lopez, that was Orion and he informed me that Artie now has the new Intersect v 2.1 in his head."

**Puck**

"Not Neil!"

**Sue**

"We need you to convince Orion to put the rest of the Intersect back Colonel Puckerman."

**Puck**

"Yes, General."

**Sue**

"But first, you three have a plane waiting on you to take you to London for Agent Karofsky's funeral. And since Agent Lopez is staying I will send another agent to find Sebastian Larkin."

_A brief moment of grief and anger passed through the room._

**Artie**

"I still cannot believe Sebastian would just kill Dave like that."

**Santana**

"Artie, Sebastian was a double agent, none of us knew."

**Sue**

"Well actually we did. That is why we were sending you with him Agent Lopez. We wanted you to find out about his new organization POGO."

**Puck**

"What's POGO General?"

**Sue**

"People for the Overthrow of Governmental Officials, his main goal at the wedding was to put the Intersect back in Artie's head and turn him, so he could use him to overthrow the NSA and CIA. You should probably be leaving. I expect a full report by Thursday Colonel."

**Puck**

"Yes General."

**London**

_The funeral was very sweet and memorable. But what was more memorable was that night. Though they had three separate room that did not stop Santana from breaking into Artie's room and try to spend the night with him wearing a robe._

**Artie**

"Santana! What are you doing?"

**Santana**

"Spending the night with the man I love. Do you have a problem with that?"

_The robe falls to the ground revealing the sexy lingerie he had seen in a dream right after seeing her shoot the Fulcrum agent on Christmas._

**Artie**

"Nope, no problems here." _(He looks up and whispers) "Thank you God"_

_The door fiercely swings open, Puck comes storming in._

**Puck**

"I have a problem with it."

**Santana**

"Puck how did you know?"

**Puck**

"Lopez did you actually believe I didn't have this room bugged while we were at the funeral? I know you had mine bugged."

**Santana**

"I did no such thing."

_At that moment room service comes in. Upon hearing the bellboy's voice Artie flashes._

**Artie**

"Santana, Fulcrum has operatives in M-I6, and one of them are in front of us."

_Upon hearing this Santana gives Puck the signal and the bellboy was unconscious in no time._

**Puck **

"We need to call the General."

**Santana**

"First we need to sweep the room and make sure it is secure."

**Puck**

"Agreed."

_They clear the room of all surveillance devices, call General Sylvester and arrange immediate transport back to the States._

**Los Angeles**

_Artie, Santana and Puck are at Will Schuester's cover business that used to be Roark Inc. they are in a secret underground lab that Will had set up so that no one could use any surveillance device to hear or find his location._

**Will**

"So, old Sue wants me to put the whole intersect back in Artie's head."

**Puck**

"That is correct."

**Will**

"Well, no I refuse to do it unless she gives me full immunity and gives the newly renamed New Directions Incoporated all government contracts."

**Puck**

"Let me call her."

_Puck calls Sue and gives her all the demands. She is reluctant at first but agrees to his demands_

**Puck**

"She is in."

**Will**

"Okay, lets do this."

_Artie goes through the familiar process and is once again the full Intersect._

**Will**

"Before I forget, I added some hand to hand combat knowledge and basic survival skills to the Intersect."

**Artie**

"What does that mean?"

_Will punches Artie and is on the ground in agony in under a minute._

**Puck**

"Awesome!"

**Santana**

"So Artie in now trained in combat?"

**Will**

_(Out of breath) _"Yes he is. He now has more training then you Ms. Lopez."

**Santana**

"I doubt that."

**Artie**

"Try me or are you scared you'll get beat up by a _**nerd**_."

_Santana lunges at Artie, a short battle ensues ending with Santana pinned to the ground_

**Puck**

_(Sarcastically)_"Looks like the pants in the relationships have changed hands."

_Artie helps Santana up._

**Santana**

"Shut up Puck."

**Orange Orange**

_When they arrive at castle the Orange Orange sign is being take down and replaced by a Noah's Steakhouse. Wondering what is going on the trio immediately go to Puck's to talk to Sue._

**Puck**

"General, what is happening to our base of operations?"

**Sue**

"Since Artie quit the Buy More and his father has started working with the NSA. Artie will now be working at New Directions to help keep an eye on things. And since Fulcrum thinks the Buy More is our base of operations we want to keep an eye on it. Also we have received word that after we destroyed Black Rock they moved their operation closer to the Buy More."

**Artie**

"How close?"

**Sue**

"The Large Mart in Burbank."

**Santana**

"That still doesn't explain the steakhouse."

**Artie**

"Santana don't you get it? Noah's Steakhouse. Puck will be working there."

**Sue**

"That is correct Mister Abrams. Noah you know own and operate a steakhouse."

**Puck**

"It would be my honor General."

**Artie**

"One more thing General, stop calling me Mister Abrams. It looks like we will be working together for some time so call me Artie."

**Sue**

"Okay, I will do that Mist.. I mean Artie."

**Artie**

"Thank you ."

**Sue**

"Your welcome. Before you leave I have one more assignment for you Noah."

**Puck**

"What is it General?"

**Sue**

"Since it looks like Operation Abrams is permanent, I need you to help Artie and Santana move into their new house."

**Artie**

"General are you finally giving me permission to act on my feelings?"

**Sue**

"No Artie. This apartment is state of the art and will be monitored at all hours. I have even rented out one of the rooms to an old friend of mine, Colonel Noah Puckerman."

**Puck**

"I have to live with the numskull?"

**Sue**

"Only until I decide what to do about the Artie/Santana relationship situation. Don't get me wrong I am tired of missions getting screwed up because of your sexual tension, but, I have to bring it to my higher ups for approval."

**Santana**

"Thank you General."

_A/N: So this is Chapter 1. What do you guys think?_


	3. Honeymoon's Over

**Hudson Residence**

_Rachel has finally come to terms with the newest tenants of Casa De Hudson. It may be weird but having another newlywed bride in the house was actually comforting._

**Rachel**

"Breakfast is ready."

**Finn**

"That is awesome babe."

_Yelling can be heard from the other room_

**Sugar**

"I wish I never went to Vegas with you and got married."

_Sugar storms off_

**Rory **_(Following her)_

"Come on babe, I love you. Hey Finn, how is it going?" _(he continues out the door trying to catch Sugar)_

**Finn**

"I sure am glad we're not them babe."

**Rachel**

"Finn I have to miss dinner tonight because I am working a double today."

**Finn**

"That's cool babe we can reschedule."

**Rachel**

"I know but there was something I was going to tell you tonight. I'm pregnant!"

_Finn was caught off guard with this news. He wasn't even ready to be a father yet. He though about it for a moment_

**Rachel**

"I should have known, you aren't even ready for this."

**Finn**

"No babe, This is AWESOME! You have a little awesome in the oven now. Have you told Artie and Santana yet?"

**Rachel**

"No, now is not the time remember Santana is getting transferred to an Orange Orange on the east coast."

**Finn**

"Oh yeah, that is so not awesome. Well maybe I should take Artie cliff jumping to cheer him up."

**Rachel**

"No that is a terrible idea."

_Artie and Santana enter_

**Artie**

"Hey guys, Orange Orange tanked and Santana is staying, we decided to move in together."

_Rachel runs and hugs Artie and Santana_

**Rachel**

"That is great. I'm pregnant."

_Artie has a shocked look on his face_

**Artie**

"Awesome did she just say what I think?"

**Finn**

"Yep, you're gonna be an uncle Artie."

**Santana**

"Congratulations Rachel."

**Artie**

"So how is the other happy couple?"

**Rachel**

"Well Rory is still in culinary school and Sugar is not happy about him hanging with Mike and Tina all the time."

**Buy More of Burbank**

_With the three most productive employees quitting the Buy More suffered in sales. Seeing this the higher ups fired Emmitt, and gave Beiste back his job and allowed him to pick his own assistant manager._

**Beiste**

"So how does it feel to be Buy More brass?"

**Santana**

"It feels good. But why did you pick me? I just started working here today."

_Beiste looks around at the knuckleheads that wok at this store. He sees Mike and Tina trying to pull the mammocam and shakes his head._

**Beiste**

"One, you are the most competent employee I have and two, I owed Artie a favor. So, that is why I chose you."

**Santana**

"Well thank you sir."

**Beiste**

"With me marrying Rory's mom, we are kinda like family so call me Beiste."

**Santana**

"Okay Beiste will do."

**Tina**

"Sir, there is a gentleman here to see you."

**Mike**

"Yeah, and he is a total stud."

_In walks Beiste's Ex_

**Beiste**

"Jack what are you doing here?"

**Jack**

"I want you back Beiste."

**Beiste**

"Well I am happy now and I am getting married right after the divorce is final."

**Jackie**

"We'll see about that."

_He storms off_

**Tina**

"Wow sir you sure know how to pick them."

**Beiste**

"Like I have always said once they go Beiste, that's all they like. And Santana I want you to know I have always thought you and Artie were meant for each other."

_A sly smile came across her face at the thought of her and Artie together_

**Santana**

"Thank you Beiste."

_A/N: Guys I need some feedback. There is only 1 more chapter after this before I decide to continue or not and your feedback makes my decision. So do I continue or just end it?_


	4. Scorned Lovers

**Casa De Abrams**

_It was noon and Artie was just getting up. The perk of working for his father was that he got to choose his own hours. Santana and Puck have already went to work. Just as he gets out of the shower he hears a noise coming from the den. Artie checks the security cams and finds no one. So he decides to go and investigates. When he reaches the den he finds two burglars. He neutralizes them easily, when he takes off their masks he is shocked to discover that it is Lauren and Shelby._

**Artie**

"What brings you to my humble abode."

**Lauren**

"The DEA was working with the French government to bring down a jewelry ring and we received a tip that it was based here."

**Artie**

"You heard that Puck was living here didn't you?"

**Shelby**

"Yes, we were hoping to see him so we broke in. We did not realize you were living here too."

**Artie**

"The whole team lives here. Sue is trying to keep me and Santana apart so she made Puck move in with us."

**Lauren**

"I told you she wanted you Artie."

**Artie**

"I know. Well I have to meet my father for lunch. Would you like to join us? I know this great steakhouse."

**Shelby**

"Sure."

**Lauren**

"Thanks Artie."

**Artie**

_(Whispering) _"No thank you, I just hope that Puck doesn't kill me."

_They jump in his exact replica of the batmobile and drive off._

**Noah's Steakhouse**

_On the way to the steakhouse Artie calls Santana and tells her everything. She agrees to meet him there because she doesn't want to miss this. When they arrive Artie leads the two to a private booth near the kitchen where his father is waiting._

**Will**

"Hello ladies, I am Will Schuester and you are?"

**Artie**

"This is Lauren and Shelby, they are old friends of Noah's."

**Will**

"Well it was a pleasure to meet both of you."

_They all sit down and shortly there after Santana arrives._

**Santana**

"Long time no see Lauren."

**Lauren**

"So from what I hear from you still can't keep your personal life and your work separate."

_Santana gives Artie a nasty glare_

**Santana**

"Shelby it is also nice to see you again."

**Shelby**

"Likewise."

_Artie stops a waiter_

**Artie**

"Can you tell your boss that Mr. Carmichael has arrived."

**Waiter**

"Yes sir."

_Moments later Puck comes out from the back only to see his two lovers with Artie and the gang._

**Puck**

"Hello ladies, welcome to my restaurant. If you would excuse me and Artie for a moment."

_Puck yanks Artie up and drags him to the back. Santana follows._

**Puck**

"What the hell are you doing?"

**Artie**

"I found these two in our den and thought you would want a reunion."

_Santana Artieles_

_**Puck**_

"This isn't funny!"

**Santana**

"Yeah it is."

**Puck**

"How would you two like it if…"

_Just then Sebastian and Kurt come in and try to take Will, Lauren and Shelby try to fight them but they take him anyway._

_**Puck**_

"What are the odds of that."

**Casa De Abrams**

_The team returns to their house to confront Sue about the abduction of Orion. Lauren and Shelby tag along hoping to help._

**Puck**

"General you know Lauren, and this is Shelby."

**Sue**

"I know who they are. I sent them to investigate a call we received that stated Sebastian was in the area. How did you find them?"

**Artie**

"I found them in the den and took them down."

**Sue**

"That is funny. What really happened?"

**Lauren**

"We broke in and Artie found us."

**Artie**

"Let's get to business. Did you know that Kurt was working with Sebastian?"

**Sue**

"Unfortunately, how did you find out?"

**Santana**

"Sebastian and Kurt kidnapped Orion during lunch. We tried to stop them but the tranqed us."

**Sue**

"Well it looks like you will all be working together to retrieve Orion safely by any means necessary. Artie I want you to stay home for this one. You are too emotionally involved in this mission."

**Artie**

"This is my father we are talking about. I am going."

**Sue**

"That may be true. But he was kidnapped by your old college buddy and your ex best friend so for the safety of the operation you stay home. That is an order Abrams."

**Artie**

"Yes general."

**Sue**

"Okay if that is all, I want the rest of you to prepare for this mission. Sebastian and Kurt are a very dangerous duo. You will leave at twenty-one hundred hours."

**Puck's room**

_Before leaving Lauren and Shelby corner Puck in his room and confront him._

**Puck**

"What can I do for you ladies?"

**Lauren**

"What I want to know is how do you know miss French spy here?"

**Puck**

"I can explain."

**Shelby**

"I hope you can because I though we had something. I loved you."

**Puck**

"You see I like both of you but I am a one woman man. And that women is the US Government."

**Lauren**

"That is the biggest load of crap I have heard Noah Puckerman."

**Shelby**

"Same here."

**Puck**

"Ladies lets not let our feelings get in the way of this mission."

**Lauren**

"Why is Artie's dad so important to the NSA anyway?"

**Shelby**

"And why did everyone keep referring to him as Orion? I thought his name was Will."

**Puck**

"That is on a need to know basis, and you do not need to know."

_There was an awkward tension in the air as they went to the den and met with Santana._

**Santana**

"Time to go"

_As they drove away Artie started to devise his plan to rescue his father._

_A/N: So this is the last of the test chapters. I am going to give it 3 days and see what the reviews are like, if they are not great I will post the final chapter for this part of the story then call it quits or delete it all together._


	5. The Final Showdown

**Casa De Abrams**

_Just as Artie had loaded his supplies and was about to leave to rescue his father, his phone rang._

**Artie**

"Hello."

**Sebastian**

"We know your team is on their way. We will kill them and Orion if you do not meet with us personally."

**Artie**

"I have no idea what you are talking about Sebastian. What I do know is if one hair on Orion's head is out of place you will be dead."

**Kurt**

"Oh Artie, you were never good at lying. Just meet us at the old arcade downtown in an hour or your friends are dead. I will kill Santana personally."

**Artie**

"Kill them then see if I care."

**Sebastian**

"You are making the biggest mistake of your life Artie."

**Artie **

"You have no idea Sebastian."

**Abandoned Mall**

_As the team arrives they feel that something is wrong._

**Santana**

"Something just doesn't feel right. There are no guards anywhere. It is like they knew we were coming and left."

_Lauren and Shelby pull their guns on Puck and Santana_

**Lauren**

"We are the guards."

_Just then two shots are heard. Lauren and Shelby fall to the ground. They were dead. Puck and Santana stood there wondering where the shots came from. Then they hear an all to familiar voice from behind them._

**Artie**

"That was surprisingly easy."

**Puck**

"Where did the nerd learn to shoot a sniper rifle?"

**Artie**

"Looks like there are some more little gifts my father put into the Intersect."

**Puck**

"Bout time Abrams started pulling his weight around here."

**Santana**

"Quiet Puckerman. What are you doing here Artie, Sue told you to stay home."

**Artie**

"Did you really think that would happen. I didn't want to miss out on al the fun. Besides if I didn't show up when I did you would be dead right now."

**Puck**

"Thanks Abrams, I owe you one."

_Just then an eerie voice comes from the second floor._

**Sebastian**

"Looks like our buddy has learned a few tricks Santana. It doesn't matter you will all be dead soon anyways."

_Like a sixth sense Artie felt the inventible danger behind them and reacted. Puck and Santana turn to discover Kurt unconscious on the floor._

**Santana**

"How did you know he was there?"

**Artie**

"I just figured since she was nowhere to be seen, that he must be behind us and reacted accordingly."

_Sebastian is now running out of the mall._

**Puck**

"Artie I will take care of this, you and Santana go get your father and take care of Sebastian."

**Artie**

"Thanks Puck."

_Once Artie and Santana get outside of the mall they cannot decide on who will go after Sebastian._

**Artie**

"Santana this is my fight, I will take care of Sebastian once and for all."

**Santana**

"Artie I am the agent here, you worry about finding your father."

**Artie**

"There is only one way to settle this, I will fight you for it."

_Knowing she will lose, Santana agrees to let Artie go after Sebastian. Artie looks everywhere but cannot find Sebastian._

**John's Steakhouse**

_After successfully saving Papa S, but getting chewed out by General Sylvester for losing Sebastian the team goes out for a celebratory dinner._

**Puck**

"So Sebastian is still out there somewhere."

**Santana**

"At least we killed two of his operatives, and captured Kurt."

**Artie**

"Hey buddy, sorry about your ladies being killed."

**Puck**

"They turned on their countries and got what they deserved."

**Artie**

"Still, Shelby was the love of your life. If you need me to run the restaurant for awhile so you can take some time to grieve I will."

**Puck**

"Thanks Abrams, but that will not be necessary. I am okay."

**Casa De Abrams**

_A couple of weeks later, Rory and Sugar come over for dinner._

**Rory**

"We have some exciting news."

**Sugar**

"I'm Pregnant!"

**Rory**

"So, buddy you're gonna be an uncle."

**Santana**

"Congratulations guys. When are you due?"

**Sugar**

"A couple of weeks after Rachel."

**Artie**

"Have you told Rachel?"

**Rory**

"Unfortunately, now this is all they can talk about. Hey Artie, lets leave the ladies alone to talk and go play some Call of Duty for old time sakes."

**Artie**

"Okay buddy."

_They go to the game room in the attic_

**Rory**

"Before I forget someone called for you the other day at the apartment. They were talking about some sand wall at Brittany's Deli."

_Even before he flashed Artie knew what sand wall was and knew that Sebastian had found out about Brittany._

**Brittany's Deli**

_When Artie arrived at the plaza he was immediately stopped by Puck._

**Puck**

"What are you doing here Artie? You are supposed to be finishing the new prototype for the military."

**Artie**

"He's here Puck and he wants to hurt Brittany."

**Puck**

"You and Brittany broke up over a year ago. The only way he could have found out about her is. Artie stay right here, I will be right back."

_Artie was still afraid of Puck so he waited for his return._

**Puck**

"It was just as I thought. The beta Intersect was stolen. Luckily no information was added to it after the whole Buy More robbery incident."

**Artie**

"So that is how he knew about Brittany. I have to save her."

**Santana**

"Not without backup."

**Puck**

"I took the liberty of calling her and filling her in on the situation."

**Artie**

"Thanks guys, but after Brittany is safe you leave. Sebastian is mine and mine alone."

_They were hesitant, but they agreed to the terms. They enter the deli and Sebastian freely hands over Brittany. As promised Santana and Puck took Brittany to Safety._

**Sebastian**

"So Artie we are finally alone."

**Artie**

"Just the way I wanted it."

_Sebastian pulls his gun._

**Artie**

"What, you afraid to take me on like a man Sebastian?"

**Sebastian**

"If that is the way you want it, then that is the way it will be." _(Sebastian drops his gun) _"You don't expect to beat me do you Artie?"

_A small scuffle ensues and Sebastian finds himself on the ground._

**Sebastian**

"How did you do that."

**Artie**

_(Tapping his head)_"I got an upgrade. Now I have many more skills."

**Sebastian**

"So it was you that killed those two at the mall. I searched everywhere for a sniper and never found one."

**Artie**

"Yeah, I killed them and you are next."

_In what seemed like a flash Artie acrobatically got the gun and shoots Sebastian. As Sebastian lays there dying he imparts one last thing to Artie._

**Sebastian**

"I did all this so that you would join me and we could fight Fulcrum together."

**Artie**

"We could have done that if you wouldn't have kidnapped my father."

**Sebastian**

_(with his dying breath)_"It all makes sense now, the Intersect was created for you."

_Just to make sure he was dead Artie shot Sebastian in the head. Puzzled by Sebastian's dying words Artie exited the deli. Outside Puck, Santana and Brittany were waiting for him._

**Brittany**

"Thank you for saving me Artie."

**Artie**

"I know it has been awhile, but can we be friends?"

**Brittany**

"I will do you one better. I am officially putting the Artie Abrams back on the menu. And to say thank you to your friends I will name a sandwich after them too."

**Artie**

"Thanks, I have really missed that sandwich. Well you should probably head home and get some sleep."

**Brittany**

"See you later Artie."

**Artie**

"You said it Britt."

_As she walks away Brittany is laughing. Artie turns to Santana, who has the biggest look of disgust on her face._

**Artie**

"What? She's only a friend."

_He leans over and kisses her on the cheek._

**Santana**

"I will forgive you for her, but the bad rhyme is another thing."

_Seeing Santana was content he tells them about what happened._

**Artie**

"Tell Sue POGO is gone."

**Santana**

"Sebastian is finally gone?"

**Artie**

"I shot him in the head to make sure."

**Puck**

"Why didn't I think of that."

**Santana**

"We need to tell the General everything. Lets go."

**Artie**

"I am going to sit this one out. I have some business to take care of."

_As Artie watches his team drive off and the cleaning crew arrive, he knew what he had to do now._

_A/N: Well, I am just going to call this one done. I still have 39 more chapters for this story, but it bombed and I decided just to end it right here with 1 out of 7 plausible endings I had for this story. Sorry guys._


End file.
